Closed alberskib closed 10 years ago
wait, today is only 06.07.2014. are you from the future??? o_o
Generally, I am preparing questions for nearest meeting - that's all. In other words: I am planning to ask this question in 09.07.2014 :) After meeting I will add notes.
Ah, ok ") sorry, I was a bit confused..
:question: :neutral_face: What question?
Notes:
@pablopareja
In Gene onthology there is also next type of relationship: occurs_in
but in model this kind of relationship is not present - it is something deprecated?
Hey! I just downloaded and checked out the last version of the OBO-XML file and there's no hit for that relationship. Where did you get that relationship type from?
When you open file: http://geneontology.org/ontology/go.obo and search relationship: occurs_in
you will find ie. entry with GO:0000963
id that has this relationship declared in file
You're right but so far we've been using the OBO-XML format; http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz And there you cannot find any occurrence of that relationship... I have no idea why... One of them must be either wrong or outdated :confused:
I also find occurs_in
relationship in next file: http://purl.obolibrary.org/obo/go.owl.
On next page http://www.geneontology.org/page/download-ontology OBO-XML is under legacy downloads
section.
@pablopareja @alberskib see Cross products in the GO docs. It's something that as far I know no tool relying on GO uses; kind of an experiment at this point.
Also GO Ontology relations, this could be outdated though
In the file http://purl.obolibrary.org/obo/go.owl. occurs_in
can be found about 6 times in relationship tag and much more in intersection tag.
To sum up which format is outdated?
None of them :) it's the data. The standard GO distribution only considers the relations that we already have; all the others (like occurs_in
) are part of the extended GO distribution.
OK Great to know. Thanks
Questions:
has part
,part of
,is a
,regulates
,negatively regulates
,positively regulates
what about others ie.occurs in